This directory contains a dump of the UCSC genome annotation database for the
Jun 2013 (Macaca_fascicularis_5.0/macFas5) assembly of the crab-eating macaque genome
(macFas5, Washington University (WashU) GCA_000364345.1) .
The annotations were generated by UCSC and collaborators worldwide.
For more information about this assembly, please note the NCBI resources:
http://www.ncbi.nlm.nih.gov/genome/776
http://www.ncbi.nlm.nih.gov/genome/assembly/704988
http://www.ncbi.nlm.nih.gov/bioproject/215851
Files included in this directory (updated nightly):
- *.sql files: the MySQL commands used to create the tables
- *.txt.gz files: the database tables in a tab-delimited format
compressed with gzip.
To see descriptions of the tables underlying Genome Browser annotation
tracks, select the table in the Table Browser:
http://genome.ucsc.edu/cgi-bin/hgTables?db=macFas5
and click the "describe table schema" button. There is also a "view
table schema" link on the configuration page for each track.
---------------------------------------------------------------
If you plan to download a large file or multiple files from this
directory, we recommend you use ftp rather than downloading the files
via our website. To do so, ftp to hgdownload.soe.ucsc.edu, then go to
the directory goldenPath/macFas5/database/. To download multiple
files, use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
Alternate methods to ftp access.
Using an rsync command to download the entire directory:
rsync -avzP rsync://hgdownload.soe.ucsc.edu/goldenPath/macFas5/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.soe.ucsc.edu/goldenPath/macFas5/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/macFas5/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/macFas5/database/gc5BaseBw.txt.gz'
-O gc5BaseBw.txt.gz
Please note that some files contents, such as this example gc5BaseBw.txt.gz,
will point to the data being hosted in another /gbdb/ location, which
refers to ftp://hgdownload.soe.ucsc.edu/gbdb/
To uncompress the *.txt.gz files:
gunzip <table>.txt.gz
The tables can be loaded directly from the .txt.gz compressed file.
It is not necessary to uncompress them to load into a database,
as shown in the example below.
To load one of the tables directly into your local mirror database,
for example the table chromInfo:
## create table from the sql definition
$ hgsql macFas5 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql macFas5 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
The Crab-eating macaque sequence is made freely available to the community by the
Genome Sequencing Center, Washington University School of Medicine, with
the following understanding:
1. The data may be freely downloaded, used in analyses, and repackaged in
databases.
2. Users are free to use the data in scientific papers analyzing these data
if the providers of these data are properly acknowledged. See
http://genome.ucsc.edu/goldenPath/credits.html for credit information.
3. The centers producing the data reserve the right to publish the initial
large-scale analyses of the data set, including large-scale identification
of regions of evolutionary conservation and large-scale genomic assembly.
Large-scale refers to regions with size on the order of a chromosome (that
is, 30 Mb or more).
4. Any redistribution of the data should carry this notice.
-----------------------------------------------------------------------------
GenBank Data Usage
The GenBank database is designed to provide and encourage access within
the scientific community to the most up to date and comprehensive DNA
sequence information. Therefore, NCBI places no restrictions on the use
or distribution of the GenBank data. However, some submitters may claim
patent, copyright, or other intellectual property rights in all or a
portion of the data they have submitted. NCBI is not in a position to
assess the validity of such claims, and therefore cannot provide comment
or unrestricted permission concerning the use, copying, or distribution
of the information contained in GenBank.
-----------------------------------------------------------------------------
All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
gc5BaseBw.txt.gz 2016-04-07 12:59 63
ncbiRefSeqOther.txt.gz 2020-05-10 03:28 75
extNcbiRefSeq.txt.gz 2020-05-10 03:28 91
bigFiles.txt.gz 2024-12-08 03:35 94
grp.txt.gz 2016-04-07 12:44 206
history.txt.gz 2016-04-07 12:44 887
hgFindSpec.txt.gz 2024-07-25 09:34 1.3K
gc5BaseBw.sql 2016-04-07 12:59 1.3K
ncbiRefSeqOther.sql 2020-05-10 03:28 1.3K
ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K
ensPep.sql 2020-08-31 16:00 1.3K
grp.sql 2016-04-07 12:44 1.3K
ncbiRefSeqPepTable.sql 2020-05-10 03:28 1.4K
ensemblSource.sql 2020-08-31 16:00 1.4K
chromInfo.sql 2016-04-07 12:59 1.4K
bigFiles.sql 2024-12-08 03:35 1.4K
ensemblToGeneName.sql 2020-08-31 15:39 1.4K
chromAlias.sql 2018-02-04 08:05 1.4K
ucscToINSDC.sql 2018-02-04 08:05 1.4K
ucscToRefSeq.sql 2018-02-04 08:05 1.4K
extNcbiRefSeq.sql 2020-05-10 03:28 1.4K
ensGtp.sql 2020-08-31 15:39 1.4K
tableDescriptions.sql 2024-12-07 02:03 1.5K
windowmaskerSdust.sql 2016-04-07 12:59 1.5K
microsat.sql 2016-04-07 12:59 1.5K
cytoBandIdeo.sql 2016-04-07 12:59 1.5K
chainHg19Link.sql 2016-04-07 12:44 1.5K
chainHg38Link.sql 2016-04-07 12:47 1.5K
seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K
chainPapHam1Link.sql 2016-04-07 12:51 1.5K
chainTarSyr2Link.sql 2016-04-07 12:53 1.5K
chainCalJac4Link.sql 2020-11-03 01:51 1.6K
history.sql 2016-04-07 12:44 1.6K
tableList.sql 2024-12-08 03:35 1.6K
gap.sql 2016-04-07 12:59 1.6K
gbLoaded.sql 2020-08-19 14:53 1.6K
gold.sql 2016-04-07 12:44 1.7K
genscan.sql 2016-04-07 12:59 1.7K
cpgIslandExt.sql 2016-04-07 12:59 1.7K
chainHg19.sql 2016-04-07 12:44 1.7K
chainHg38.sql 2016-04-07 12:45 1.7K
chainPapHam1.sql 2016-04-07 12:51 1.7K
chainTarSyr2.sql 2016-04-07 12:51 1.7K
cpgIslandExtUnmasked.sql 2016-04-07 12:59 1.7K
refFlat.sql 2020-08-19 14:40 1.7K
chainCalJac4.sql 2020-11-03 01:39 1.7K
xenoRefFlat.sql 2020-08-19 14:40 1.7K
estOrientInfo.sql 2016-04-07 12:59 1.8K
hgFindSpec.sql 2024-07-25 09:34 1.8K
mrnaOrientInfo.sql 2020-08-19 14:23 1.8K
rmsk.sql 2016-04-07 13:00 1.9K
simpleRepeat.sql 2016-04-07 13:01 1.9K
ncbiRefSeq.sql 2020-05-10 03:28 1.9K
augustusGene.sql 2016-04-07 12:44 1.9K
ensGene.sql 2020-08-31 15:39 1.9K
refGene.sql 2020-08-19 14:37 1.9K
ncbiRefSeqCurated.sql 2020-05-10 03:28 2.0K
xenoRefGene.sql 2020-08-19 14:40 2.0K
ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K
ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K
trackDb.sql 2024-07-25 09:34 2.1K
netHg19.sql 2016-04-07 12:59 2.1K
netHg38.sql 2016-04-07 12:59 2.1K
netPapHam1.sql 2016-04-07 12:59 2.1K
netTarSyr2.sql 2016-04-07 13:00 2.1K
all_est.sql 2016-04-07 12:44 2.1K
intronEst.sql 2016-04-07 12:44 2.1K
refSeqAli.sql 2020-03-01 07:36 2.1K
ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K
netCalJac4.sql 2020-11-03 01:54 2.1K
all_mrna.sql 2020-08-19 14:23 2.1K
xenoRefSeqAli.sql 2020-08-19 14:40 2.1K
tableList.txt.gz 2024-12-08 03:35 3.7K
tableDescriptions.txt.gz 2024-12-07 02:03 7.6K
cytoBandIdeo.txt.gz 2016-04-07 12:59 38K
chromInfo.txt.gz 2016-04-07 12:59 40K
gbLoaded.txt.gz 2020-08-19 14:53 44K
ucscToINSDC.txt.gz 2018-02-04 08:05 57K
ucscToRefSeq.txt.gz 2018-02-04 08:05 60K
trackDb.txt.gz 2024-07-25 09:34 68K
chromAlias.txt.gz 2018-02-04 08:05 82K
ensemblSource.txt.gz 2020-08-31 16:00 145K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:28 165K
refFlat.txt.gz 2020-08-19 14:40 187K
refGene.txt.gz 2020-08-19 14:37 200K
refSeqAli.txt.gz 2020-03-01 07:36 207K
ensemblToGeneName.txt.gz 2020-08-31 15:39 249K
mrnaOrientInfo.txt.gz 2020-08-19 14:23 258K
microsat.txt.gz 2016-04-07 12:59 373K
ncbiRefSeqCds.txt.gz 2020-05-10 03:28 435K
ensGtp.txt.gz 2020-08-31 15:39 486K
cpgIslandExt.txt.gz 2016-04-07 12:59 607K
all_mrna.txt.gz 2020-08-19 14:23 1.0M
gap.txt.gz 2016-04-07 12:59 1.1M
seqNcbiRefSeq.txt.gz 2020-05-10 03:28 1.1M
cpgIslandExtUnmasked.txt.gz 2016-04-07 12:59 1.5M
gold.txt.gz 2016-04-07 12:44 1.5M
estOrientInfo.txt.gz 2016-04-07 12:59 1.8M
ncbiRefSeqLink.txt.gz 2020-05-10 03:28 2.0M
augustusGene.txt.gz 2016-04-07 12:44 2.2M
genscan.txt.gz 2016-04-07 12:59 2.9M
ensGene.txt.gz 2020-08-31 15:39 3.2M
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 3.6M
ncbiRefSeq.txt.gz 2020-05-10 03:28 3.7M
ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 5.3M
intronEst.txt.gz 2016-04-07 12:44 7.1M
ensPep.txt.gz 2020-08-31 16:00 7.4M
all_est.txt.gz 2016-04-07 12:44 9.7M
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:28 10M
chainHg19.txt.gz 2016-04-07 12:44 15M
netPapHam1.txt.gz 2016-04-07 12:59 19M
netHg19.txt.gz 2016-04-07 12:59 21M
netHg38.txt.gz 2016-04-07 12:59 22M
chainPapHam1.txt.gz 2016-04-07 12:51 24M
simpleRepeat.txt.gz 2016-04-07 13:01 25M
xenoRefFlat.txt.gz 2020-08-19 14:40 30M
xenoRefSeqAli.txt.gz 2020-08-19 14:40 32M
xenoRefGene.txt.gz 2020-08-19 14:40 33M
netCalJac4.txt.gz 2020-11-03 01:54 49M
netTarSyr2.txt.gz 2016-04-07 13:00 67M
chainPapHam1Link.txt.gz 2016-04-07 12:51 84M
windowmaskerSdust.txt.gz 2016-04-07 12:59 104M
rmsk.txt.gz 2016-04-07 13:00 135M
chainHg19Link.txt.gz 2016-04-07 12:45 177M
chainHg38.txt.gz 2016-04-07 12:46 256M
chainTarSyr2.txt.gz 2016-04-07 12:52 291M
chainCalJac4.txt.gz 2020-11-03 01:39 435M
chainHg38Link.txt.gz 2016-04-07 12:48 783M
chainTarSyr2Link.txt.gz 2016-04-07 12:54 1.2G
chainCalJac4Link.txt.gz 2020-11-03 01:51 1.3G